Genomics enthusiast
NGS data analysis pipline constructorMain
Yi-Wen Hsiao
PhD candidate in Biostatistics at National Taiwan University.
I have been trained in bioinformatics, engineering and biotechnology, with both experimental and computational skills developed from extensive research experience.
My current research interests involve highly dimensional data analysis, text-mining technology, artificial intelligence/machine learning and their application in the biological field.
Education
Doctoral Candidate in Biostatistics
National Taiwan University - College of Public Health - Institute of Epidemiology and Preventive Medicine
Taipei, Taiwan
2019 - present
- Attended Courses: Mathematical Statistics, Statistical Analysis for Repeated Measurements, Statistical and Machine Learning
- Proposed research project: Identification of Genetic-based Prognostic Biomarkers via Next-generation Sequencing Data for Cancer Patients
- Scholarship: Taiwanese Excellent Doctor scholarship (2019-2023)
- Advisor: Dr Tzu-Pin Lu
- Current GPA: 4.00/4.30
Master in Biotechnology
Newcastle University - School of Natural and Environmental Sciences
Newcastle, United Kingdom
2014 - 2015
- Graduate Program in Industrial and Commercial Biotechnology
- Grade: Merit
- Dissertation:Ribosome engineering to improve antimicrobial production
- Advisor: Dr James Stach
Master in Chemical Engineering
National Chung Cheng University - College of Engineering
Chiayi, Taiwan
2010 - 2013
- GPA: 4.24/5.0
- Dissertation: The Differentiation of Domapinergic Neurons from Bone Marrow-Derived Mesenchymal Stem Cells Modified by DNA Target Methylation
- Advisor: Professor Wen-Chien Lee
Bachelor in Chemical engineering
National Chung Cheng University - College of Engineering
Chiayi, Taiwan
2006 - 2010
- GPA: 3.73/5.0
Work Experience
Research Assistant
Bioinformatics and Biostatistics Core Lab - Center of Genomic and Precision Medicine - National Taiwan University
Taipei, Taiwan
2016 - 2019
- Analyszed different types of microarray and sequencing data
- Built customized analytical pipelines and reports
- Literature reviews and academic writing
Research Experience
Course Project
National Taiwan University - College of Public Health - Institute of Epidemiology and Preventive Medicine
Taipei, Taiwan
2021
- Course Name: Statistical and Machine Learning
- Course instructor: Dr Charlotte Wang
- Practical Project: Stock Trend Prediction using Machine Learning Algorithms
- Project Link: http://www.ywhsiao.com/2021-Spring-EPM-7012-Statistical-and-Machine-Learning/
Research Assistant (dry lab experience)
Bioinformatics and Biostatistics Core Lab - Center of Genomic and Precision Medicine - National Taiwan University
Taipei, Taiwan
2016 - 2019
- Conducted the reference-based mRNA-seq data analysis in terms of differential expression, variant discovery and fusion gene detection
- Also had experience in other types of RNA-seq data analysis, such as microRNA, lncRNA or circRNA
- Applied machine learning (ML) approach to predict cancer type using proteomic data
- Conducted an integrated analysis using both RNA-seq and ChIP/ATAC-seq data to understand the regulation mechanism in different T-cell types
- Identified germline or somatic mutations and CNV detection from whole-exome sequencing data using GATK3/4 pipeline for cancer research
- Integrated in-silico neoantigen prediction tools and HLA-typing software in cancer immunotherapy for customized vaccine design
- Utilized A5-miseq assembly pipeline to construct a single-strand viral genome for the discovery of point mutation after several generation
- Analyzed 16s rRNA/ITS amplicon sequencing data using QIIME1/2 pipeline to study microbial communities under different conditions
Masters Research (wet lab experience + dry lab experience)
Newcastle University - School of Natural and Environmental Sciences
Newcastle, United Kingdom
2014 - 2015
- Applied ribosome engineering approach to improve the production of antibiotic compounds in one of the novel marine bacteria
- Identified point mutation caused by antibiotic treatment using bioinformatics tool
- Evaluated antimicrobial activity and predicted the mode of action
Masters Research (wet lab experience)
National Chung Cheng University - College of Engineering
Chiayi, Taiwan
2010 - 2013
- Utilized molecular technologies, such as gel-based RT-PCR, real-time RT-PCR to evaluate whether the genes related to neural development were increased after neural induction in mesenchymal stem cell
- Used flow cytometry and western blot to detect the expression of neural proteins
Academic Articles
Race-Specific Genetic Profiles of Homologous Recombination Deficiency in Multiple Cancers
Journal of Personalized Medicine 2021, 11 (12), 1287.
N/A
2021
- YW Hsiao, TP Lu
Rare variants discovery by extensive whole-genome sequencing of the Han Chinese population in Taiwan: Applications to cardiovascular medicine
Journal of Advanced Research. 2020.
N/A
2021
- JMJ Juang, TP Lu, MW Su, CW Lin, JH Yang, HW Chu, CH Chen, YW Hsiao, CY Lee, LM Chiang, QY Yu, CK Hsiao, CYJ Chen, PE Wu, CH Pai, EY Chuang, CY Shen
A risk prediction model of gene signatures in ovarian cancer through bagging of GA-XGBoost models
Journal of Advanced Research. 2020.
N/A
2021
- YW Hsiao*, CL Tao*, EY Chuang, TP Lu
Text-mining in cancer research may help identify effective treatments
Translational Lung Cancer Research. 2019, S460-S463.
N/A
2019
- YW Hsiao, TP Lu
RNASeqR: An R package for automated two-group RNA-Seq analysis workflow
IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2019
N/A
2019
- KH Chao, YW Hsiao, YF Lee, CY Lee, LC Lai, MH Tsai, TP Lu, EY Chuang
Using proteomic profiling to characterize protein signatures of different thymoma subtypes
BMC Cancer. 2019, 19(1), pp.1-8.
N/A
2019
- LC Lai, QL Sun, YA Chen, YW Hsiao, TP Lu, MH Tsai, L Zhu, EY Chuang, W Fang
Clinicopathologic Characterization of GREB1-rearranged Uterine Sarcomas With Variable Sex-Cord Differentiation
The American journal of surgical pathology. 2019, 43(7), pp.928-942.
N/A
2019
- CH Lee, YC Kao, WR Lee, YW Hsiao, TP Lu, CY Chu, YJ Lin, HY Huang, TH Hsieh, YR Liu, CW Liang
Dual immuno-renal targeting of 7-benzylidenenaltrexone alleviates lupus nephritis via Fc_RIIB and HO-1
Journal of Molecular Medicine. 2018, 96(5), pp.413-425.
N/A
2018
- TC Tseng, DY Huang, LC Lai, H Hwai, YW Hsiao, JR Jhou, EY Chuang, SJ Tzeng
A standardized herbal extract mitigates tumor inflammation and augments chemotherapy effect of docetaxel in prostate cancer
Scientific Reports. 2017, 7(1), pp.15624.
N/A
2017
- CH Tsai, SF Tzeng, SC Hsieh, YC Yang, YW Hsiao, MH Tsai, PW Hsiao
Oral Presentations
International Conference on Intelligent Biology and Medicine ICIBM 2019
N/A
Ohio, United States
2019
- Topic: The Comparisons of Prognostic Power and Expression Level of Tumor Infiltrating Leukocytes in Hepatitis B- and Hepatitis C-related Hepatocellular Carcinomas
Taiwan Public Health Association TPHA 2019
N/A
Taipei, Taiwan
2019
- Topic: A genomewide association study of Brugada Syndrome in Taiwan
Seminar Presentations
2021 Spring Doctoral Seminar
N/A
Taipei, Taiwan
2021
- Paper Title:Pan-cancer landscape of homologous recombination deficiency Slides
2020 Spring Doctoral Seminar
N/A
Taipei, Taiwan
2020
- Paper Title:Comparison of pathway and gene-level models for cancer prognosis prediction Slides
2020 Fall Doctoral Seminar
N/A
Taipei, Taiwan
2020
- Paper Title: Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE) Slides
2019 Fall Doctoral Seminar
N/A
Taipei, Taiwan
2019
- Paper Title: Network-guided prediction of aromatase inhibitor response in breast cancer Slides
Teaching Assistant Positions
Introduction and Application of Computational Biology Methods
N/A
Taipei, Taiwan
2021
- Course instructor: Dr Tzu-Pin Lu
- Advisor: Statistics Education Center, National Taiwan University
- Duties: reply to the questions from students, correct coding homework
Biostatistics and Epidemiology
N/A
Taipei, Taiwan
2021
- Course instructor: Dr Tzu-Pin Lu
- Advisor: Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University
- Duties: deliver online practical lectures, reply to the questions from students, correct papers
Applied Biostatistics (A)
N/A
Taipei, Taiwan
2021
- Course instructor: Professor Shu-Hui Chang
- Advisor: Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University
- Duties: delivered practical lectures, replied to the questions from students, corrected papers
Applied Biostatistics (B)
N/A
Taipei, Taiwan
2021
- Course instructor: Professor Yu-Kang Tu
- Advisor: Statistics Education Center, National Taiwan University
- Duties: delivered practical lectures, replied to the questions from students, corrected papers
Applied Biostatistics (B)
N/A
Taipei, Taiwan
2020
- Course instructor: Professor Yu-Kang Tu
- Advisor: Statistics Education Center, National Taiwan University
- Duties: delivered practical lectures, replied to the questions from students, corrected papers
Workshops taught
Advanced Statistic Analysis Workshop - RNA-seq data analysis
N/A
Taipei, Taiwan
2019
- 2 hours with practice
Workshops attended
Teaching Assistant Training Program for practical statistics
National Taiwan University - Statistics Education Center
Taipei, Taiwan
2019
- A 5-day workshop
- did a demonstration for statistics with R programming
- gained a teaching certificate
Teaching Assistant Orientation
National Taiwan University - Center for Teaching and Learning Development
N/A
2019
- A 4-hour online workshop